[Biopython] sff inot fasta and qual then trim

[Peter Cock]

On Tue, Oct 23, 2012 at 6:13 PM, Kiss, Csaba <csaba.kiss at lanl.gov> wrote:
>>Could be - disk IO will be a factor, but I suspect the quality trimming to be the slow part rather than the format conversion.
>
> I don't think it's IO or the trimming. Mothur seems to take forever to do the sffinfo process on windows.
> Getting the 3 million sequences out was 3 hours.

That sounds a bit slow, can you compare this to the Biopython SFF
conversion time (or any of the other tools)?

> The trimming took 10 minutes.
> The rest of the python code to fish out my sequences 1 minute.
>
> You see now , why I would like to make it more efficient.
>
> Csaba

Is it possible to fish out your sequences and then do the trimming? If
possible that sounds like it would be more efficient.

Peter